Gusta me (GUide to STatistical Analysis in Microbial Ecology) is a website packed full of useful information for commonly employed community ecology (plus other) techniques in a microbial setting. Probably needs updating as lots of new modelling based approaches have been added in the last couple of years. Still broadly useful though as the descriptions of the techniques are spot on.
Here is the link: http://mb3is.megx.net/gustame/home
I have not read the associated paper yet – but I’m sure it could be useful too.